S.T.A.L.K.E.R have quests, loot, moral choices, stats upgraded through artifacts and equipment. Call of Pripyat have a quest structure that reminds me about Fallout 2.

— Mankind must put an end to war or war will put an end to mankind. - John F Kennedy
An eye for an eye, and soon the whole world is blind. - Mahatma Gandhi
The world is my country. To do good is my religion. My mind is my own church. This simple creed is all we need to enjoy peace on earth. - Thomas Paine

Personally, I voted for Bloodlines. Depending on what character you play it can be pretty shooter-ish, a Brujah with high levels of Celerity, for example.

Anyway, the original Bloodlines wasn't that good - it simply wasn't finished when it was released. But there's at least one fan patch out there that changes that and finally makes Bloodlines the really great game it deserves to be.

I voted FO3 but didn't play all on the list.
FO3 is my fav because of Mod community, it keeps the game alive. Played it probably hundreds of hours, installed Vegas now. I played Stalker and ME2 but those 2 games have no replay value for me.

Nearly impossible to decide…
Vampire Bloodlines for it's atmospheric world and the sheer joy of playing a malkavian.
System Shock for being one of the view games that was at it's release unnerving, atmospheric and created levels that made sense, not to mention one of the best villains I've seen so far in any computer game.
Deus Ex because it was constantly interesting and I always wanted to know what happens next in the storyline.. loved the different endings.
Last but not least Mass Effect .. well just because it's fun and I really liked some of the companions storys.